Microarray experimental design

Hi. I’m new in Bioinformatics, my background is in Computer Science and I’m taking a course to introduce myself in this area.

One of the exercises of the course is about designing an experiment in microarray technology. The experiment should find if three compounds that had been used to treat a disease, have potential adverse effects. To accomplish the experiment we have access to samples from a range of tissues taken from three mice treated by the three different compounds during 7 days.

The samples from first and second compounds were taken in seventh day and the samples of the third compound were taken in the tenth day.

I know that I need to calculate the number of samples to use in the array and number of the biological replicates, but I don’t even know which questions the experiment should answer.

I don’t want the possible solutions to the problem, I just need that someone light me a little bit.

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